Gate-based Quantum Computing for Protein Design
Bibliographic record
Abstract
Protein design is a technique to engineer proteins by modifying their sequence to obtain novel functionalities. In this method, amino acids in the sequence are permutated to find the low energy states satisfying the configuration. However, exploring all possible combinations of amino acids is generally impossible to achieve on conventional computers due to the exponential growth of possibilities with the number of designable sites. Thus, sampling methods are currently used as a conventional approach to address the protein design problems. Recently, quantum computation methods have shown the potential to solve similar types of problems. In the present work, we use the general idea of Grover's algorithm, a pure quantum computation method, to design circuits at the gate-based level and address the protein design problem. In our quantum algorithms, we use custom pair-wise energy tables consisting of eight different amino acids. Also, the distance reciprocals between designable sites are included in calculating energies in the circuits. Due to the noisy state of current quantum computers, we mainly use quantum computer simulators for this study. However, a very simple version of our circuits is implemented on real quantum devices to examine their capabilities to run these algorithms. Our results show that using $\mathcal{O}(\sqrt N)$ iterations, the circuits find the correct results among all $N$ possibilities, providing the expected quadratic speed up of Grover's algorithm over classical methods.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".